Hi Marc,
I have not used the Canon 1ds myself, so all what I know is what other users told me. And they said that they are not always satisfied in the wideangle area (vignetting etc.). This is why Zoerkendorfer got this push to make an adapter for the MM-lenses on Canon bodies.
Canon changed its lens mount (Minolta etc. too) to AF I think at the end of the 80ies. Which is around 13-16 years ago. I do not mind about the change of the lens mount though. I am not sure whether Canon thought about digital photography when they have choosen this lens-mount-size, but who knows.
I am not an engineer, so I can not say what the consequences of the different placements of the mirror box is. I also have never talked about this with Zeiss. Maybe someone else can help here out. Maybe it is a different angle the light falls on the chip when it is more backwards in the body.
I have not thought about the new Kodak-Nikon mount model though. I have not seen anything neither yet in this direction.
Fact is, that Canon is very strong in this area and will IMO always be the brand with the most aggressive price/performance ratio. But I also think that there have been reasons for buying Zeiss lenses for analogue cameras and hope there will be still some with a digital body.
I thought about a Canon for myself, but as I said, it would mean to buy a new system with new lenses. I have a N-System (analogue) and I am very happy with it, except the missing FFL and a few minor issues as with every camera. If somebody is new for both systems, it would be a tough call. If it would be sure that N-system gets supportet more in the future, I would favour Contax obviously.
I still think that there HAS TO come something on Photokina this year for th N-system (lenses and body). Everything else would not be logical. I only hope that my "logic" is the same as in the far est